diff --git a/scripts/test_suite.args b/scripts/test_suite.args index e36462b173..fc835a2c74 100644 --- a/scripts/test_suite.args +++ b/scripts/test_suite.args @@ -14,6 +14,7 @@ --add-exports org.igv/org.broad.igv.event=junit --add-exports org.igv/org.broad.igv.exceptions=junit --add-exports org.igv/org.broad.igv.feature=junit +--add-exports org.igv/org.broad.igv.feature.aa=junit --add-exports org.igv/org.broad.igv.feature.basepair=junit --add-exports org.igv/org.broad.igv.feature.bionano=junit --add-exports org.igv/org.broad.igv.feature.dranger=junit diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java index ab3726ba1e..ccda49175a 100644 --- a/src/main/java/module-info.java +++ b/src/main/java/module-info.java @@ -2,7 +2,6 @@ exports org.broad.igv; exports org.broad.igv.tools; exports org.broad.igv.ui; - exports org.broad.igv.feature.aa; requires com.google.common; requires protobuf.java; diff --git a/src/main/java/org/broad/igv/feature/aa/AminoAcidManager.java b/src/main/java/org/broad/igv/feature/aa/AminoAcidManager.java index a678de8ea4..f0c801f3ac 100644 --- a/src/main/java/org/broad/igv/feature/aa/AminoAcidManager.java +++ b/src/main/java/org/broad/igv/feature/aa/AminoAcidManager.java @@ -63,24 +63,6 @@ public class AminoAcidManager { */ static final Map AANameMap = new HashMap(20); - private static final String[] BASE_SEQUENCES = {"TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", - "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", - "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"}; - - - public static final String DEFAULT_CODON_TABLE_PATH = "resources/geneticCode.json"; - - static final String DEFAULT_TRANS_TABLE_PATH = "resources/defaultTranslationTables.json"; - - //ID of the "standard" translation table - public static final int STANDARD_TABLE_ID = 1; - - private static final String DEFAULT_CHROMO_KEY = "default"; - - private LinkedHashMap allCodonTables = new LinkedHashMap<>(20); - - private static Table genomeChromoTable = TreeBasedTable.create(); - private static AminoAcidManager instance; private AminoAcidManager() {